Sample preparation for capillary or chip-based bioassays typically consists of preparing a sample (analyte) for a particular assay by concentrating the sample by some means, such as by centrifuging or decanting and diluting with an appropriate buffer solution. For ease of identification of the components it can be particularly desirable to “tag” the sample with an appropriate tag or tracer that can be a dye that fluoresces when exposed to the appropriate wavelength of light. However, many tag-analyte complexes have a short shelf life and need to be prepared within a day or two of use. For pathogen identification for first responders and for facilities protection it is particularly desirable to have inexpensive, integrated microchemical analysis systems commercially available that are capable of rapid (typically<2 minutes), multiplexed (>20 antigens) analyses. Automated sample preparation with microliter fluid volumes, i.e., a microfluidic analysis system, can increase repeatability and speed of sample preparation and yield more consistent bioassay results. However, bioassay architectures that require the common manipulations employed in these systems, such as solvent changes, sample preparation and concentration, cannot be implemented without active flow control.